sci-biology/bamtools: Version Bump; #452234; unbundles dev-libs/jsoncpp

Package-Manager: portage-2.2.0_alpha161/cvs/Linux x86_64
Manifest-Sign-Key: 0x70EB7916

5 files changed, 102 insertions, 20 deletions

diff --git a/sci-biology/bamtools/ChangeLog b/sci-biology/bamtools/ChangeLog
index 73176ef15b8b..a209ac6bf792 100644
--- a/sci-biology/bamtools/ChangeLog
+++ b/sci-biology/bamtools/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/bamtools
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bamtools/ChangeLog,v 1.3 2012/04/26 16:44:38 jlec Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bamtools/ChangeLog,v 1.4 2013/01/28 08:35:06 jlec Exp $
+
+*bamtools-2.2.3 (28 Jan 2013)
+
+  28 Jan 2013; Justin Lecher <jlec@gentoo.org> +bamtools-2.2.3.ebuild,
+  +files/bamtools-2.2.3-unbundle.patch, metadata.xml:
+  Version Bump; #452234; unbundles dev-libs/jsoncpp
 
   26 Apr 2012; Justin Lecher <jlec@gentoo.org> bamtools-1.0.2.ebuild:
   Remove unnecessary die
diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest
index 291314d4b381..bcf5930b9090 100644
--- a/sci-biology/bamtools/Manifest
+++ b/sci-biology/bamtools/Manifest
@@ -1,14 +1,17 @@
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+Hash: SHA256
 
-DIST bamtools-1.0.2.tar.gz 207523 RMD160 ba737ad591c69d9110138dc066b9c2133ef77bb4 SHA1 70d4a1f8d7da73dd381b609b618ed19b6184366e SHA256 d3ca75d2bec531f15dbc400a76afbe48d47452ce05552c88943bbce81a0862d8
-EBUILD bamtools-1.0.2.ebuild 865 RMD160 39836acbffb25939569e2efb80e8b79238d3d8a6 SHA1 45cff426da4c8196ea9f32e389921092c931ea3d SHA256 28f29f02a2ae970cbe2929e71bb566eaa12c865d94429857fcb5dc2e30d6fbb5
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+AUX bamtools-2.2.3-unbundle.patch 1520 SHA256 4af6f0273e5035720c90d01a89b8c27f0aadc461f3b60c930f59a770a4ed18e2 SHA512 a089ba6c54b1854cf050b152b84876c0e89888ba568abfe026fb4225df92521f594e3681e842b89167bf64e7fa845be4affb8f310f158781fb3880b14256452c WHIRLPOOL db80d8dc0c1937b05c71478e92d91a62bedb86958d55fde40014499bcfb2b602df649dc2c75a29e37e7fab5198d8a7568a447e38bcddd9c80587d2527aa080a7
+DIST bamtools-1.0.2.tar.gz 207523 SHA256 d3ca75d2bec531f15dbc400a76afbe48d47452ce05552c88943bbce81a0862d8 SHA512 1934d40d50f3fdf2b1fcacb8b59cf954a3c791d3095649ac4f1246563e9d8d4afe385e42a2c6c383f0bb519eede401d12c71203d279b33e01575222f9f84c244 WHIRLPOOL 9fb4d4feb3ff867866a96533231a1b8284fd5156ab142cad727d32f8f3c157e246cca59185c3bdc253b19bde2514404a7107a62443780b060f6e8f270622c990
+DIST bamtools-2.2.3.tar.gz 538074 SHA256 92ddef44801a1f8f01ce1a397f83e0f8b5e1ae8ad92c620f2dafaaf8d54cf178 SHA512 904823605875c160c4553ec34c307583c511a3e5469f06048d44196e1d3d35dab3f582360a914fcbb3ff214316dc49e68bf57f2bb40fb854fb37dfe329d308bc WHIRLPOOL 603e233f5f3d0b546844038716f0540dbb0541e84a25cb62fb706bdfa2b16fbe491526ea5b753be0ef93eb69bb8d8f56074b6904558ef7814e0e6e1698a0ebbf
+EBUILD bamtools-1.0.2.ebuild 865 SHA256 28f29f02a2ae970cbe2929e71bb566eaa12c865d94429857fcb5dc2e30d6fbb5 SHA512 5654a0e2c9c6a88ea0894ad218caf57853685a5ceb32661c1ef25f8405f14aa87a26ca34cea88293c6ff1115f2269fdee1bf9a58ac7cfb9b38874557ddb3227f WHIRLPOOL 915c84863356b62503c4fae5d5d8475487cf34095ed92fdca391ab49326456065253b48ac182e5ec7a9eb69e16d284173c2caebd4b06b3c7a399bb89ff1ab831
+EBUILD bamtools-2.2.3.ebuild 743 SHA256 f68bfa3dacbcf4702d3a54d73b4eb021d64c379dc394e5008924f50c3b84b680 SHA512 613c2d800c6e720363c5fdd9778d8183577725800058e8852a37c83b67b6aec8596f84a729d89a99b973a66ae54d42bc41842a431d120575d0e31f2c9101e1d9 WHIRLPOOL 03bcd8a3271bb300084202b4cf60fb760283ffeb9288c6029c4d2d3830814ffdfd33fabafcc3b484ac357ea61885e43e03e2a1a6e1b65a1657c067def2ad0a57
+MISC ChangeLog 1385 SHA256 adaa7c923b92166e484520db1a59b5d7a1179d7484f40f3d4af9cd0d5f95822e SHA512 1797e3bf96e06b8b015e9b7758687ee8dd68445ce9a4c7de15e9bf42b90547cc28c8009e9d3a09fd0c61f7ca8dc835a1379a59b5cf496e763ef673639757d059 WHIRLPOOL 67474762fc9ab0d8d679185f74b88620f93fd38dab6ba85c1a29c8e117115c56b2dcc7e4485630ca08861014b0eae86777f39fd45abe3b043fa8349f478675f1
+MISC metadata.xml 663 SHA256 68b3e029b2b44a71be2e2c06197701a3f5c41e397885999bcb0a28446cd63048 SHA512 39cd07a89dffcd158dc059826c302b7558887a0a58b05f136ff2e0665d0b0f18b8d50ccd00bd87d428adf12289af0e24e3b52652aaf396068ad18747b1692a8c WHIRLPOOL 5bdf86bbf2351501e5daecec9f37c0cf52eb2f91a5f54481cb232f5cc41f951c1641209ae4c8f08d0a8ff3dee2a466a9d1fb6db7c1bcbebb3161a7ec75d7f0ea
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diff --git a/sci-biology/bamtools/bamtools-2.2.3.ebuild b/sci-biology/bamtools/bamtools-2.2.3.ebuild
new file mode 100644
index 000000000000..899c5f787d60
--- /dev/null
+++ b/sci-biology/bamtools/bamtools-2.2.3.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bamtools/bamtools-2.2.3.ebuild,v 1.1 2013/01/28 08:35:06 jlec Exp $
+
+EAPI=4
+
+inherit cmake-utils
+
+DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
+HOMEPAGE="https://github.com/pezmaster31/bamtools"
+SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="
+	dev-libs/jsoncpp
+	sys-libs/zlib"
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}"/${P}-unbundle.patch )
+
+src_install() {
+	cmake-utils_src_install
+	use static-libs || rm "${ED}"/usr/$(get_libdir)/*.a
+}
diff --git a/sci-biology/bamtools/files/bamtools-2.2.3-unbundle.patch b/sci-biology/bamtools/files/bamtools-2.2.3-unbundle.patch
new file mode 100644
index 000000000000..47d14b54c5a2
--- /dev/null
+++ b/sci-biology/bamtools/files/bamtools-2.2.3-unbundle.patch
@@ -0,0 +1,45 @@
+ src/CMakeLists.txt              | 1 -
+ src/api/CMakeLists.txt          | 4 ++--
+ src/toolkit/bamtools_filter.cpp | 2 +-
+ 3 files changed, 3 insertions(+), 4 deletions(-)
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index e359695..2bd2185 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -6,7 +6,6 @@
+ # ==========================
+ 
+ add_subdirectory( api )
+-add_subdirectory( third_party )
+ add_subdirectory( toolkit )
+ add_subdirectory( utils )
+ 
+diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt
+index 66eb35f..65f4639 100644
+--- a/src/api/CMakeLists.txt
++++ b/src/api/CMakeLists.txt
+@@ -54,8 +54,8 @@ target_link_libraries( BamTools ${APILibs} )
+ target_link_libraries( BamTools-static ${APILibs} )
+ 
+ # set library install destinations
+-install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin")
+-install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools")
++install( TARGETS BamTools LIBRARY DESTINATION "lib${LIB_SUFFIX}" RUNTIME DESTINATION "bin")
++install( TARGETS BamTools-static ARCHIVE DESTINATION "lib${LIB_SUFFIX}")
+ 
+ # export API headers
+ include(../ExportHeader.cmake)
+diff --git a/src/toolkit/bamtools_filter.cpp b/src/toolkit/bamtools_filter.cpp
+index 1189981..cf70199 100644
+--- a/src/toolkit/bamtools_filter.cpp
++++ b/src/toolkit/bamtools_filter.cpp
+@@ -16,7 +16,7 @@
+ #include <utils/bamtools_utilities.h>
+ using namespace BamTools;
+ 
+-#include <jsoncpp/json.h>
++#include <json/json.h>
+ using namespace Json;
+ 
+ #include <cstdio>
diff --git a/sci-biology/bamtools/metadata.xml b/sci-biology/bamtools/metadata.xml
index 09f78c98d172..dd28e0c5a68e 100644
--- a/sci-biology/bamtools/metadata.xml
+++ b/sci-biology/bamtools/metadata.xml
@@ -1,14 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<longdescription>BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.</longdescription>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>weaver@gentoo.org</email>
+    <name>Andrey Kislyuk</name>
+  </maintainer>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <longdescription>BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.</longdescription>
 </pkgmetadata>